NETGEN: generating phylogenetic networks with diploid hybrids

M M Morin; B M E Moret

doi:10.1093/bioinformatics/btl191

NETGEN: generating phylogenetic networks with diploid hybrids

Bioinformatics. 2006 Aug 1;22(15):1921-3. doi: 10.1093/bioinformatics/btl191. Epub 2006 May 22.

Authors

M M Morin¹, B M E Moret

Affiliation

¹ Department of Computer Science, University of New Mexico, Albuquerque, NM, USA. morin@cs.unm.edu

PMID: 16717070
DOI: 10.1093/bioinformatics/btl191

Abstract

Summary: NetGen is an event-driven simulator that creates phylogenetic networks by extending the birth-death model to include diploid hybridizations. DNA sequences are evolved in conjunction with the topology, enabling hybridization decisions to be based on contemporary evolutionary distances. NetGen supports variable rate lineages, root sequence specification, outgroup generation and many other options. This note describes the NetGen application and proposes an extension of the Newick format to accommodate phylogenetic networks.

Availability: NetGen is written in C and is available in source form at http://www.phylo.unm.edu/~morin/.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Algorithms
Biological Evolution*
Cell Lineage / genetics*
Computer Simulation
Diploidy*
Evolution, Molecular
Hybrid Cells / physiology*
Models, Genetic*
Phylogeny*
Sequence Analysis, DNA / methods*